Analysis of relative abundances on environmental gradients

Depth Gradient ◽

Negative Numbers ◽

Marine Communities ◽

Rates Of Change ◽

Compositional Approach ◽

Vertical Slice ◽

Ecologists often analyze relative abundances, which are compositions (sets of non-negative numbers with a fixed sum). However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.

Analysis of relative abundances on environmental gradients

10.7287/peerj.preprints.26908 ◽

2018 ◽

Author(s):

Fiona Chong ◽

Matthew Spencer

Keyword(s):

Compositional Data ◽

Environmental Gradients ◽

Depth Gradient ◽

Negative Numbers ◽

Marine Communities ◽

Rates Of Change ◽

Compositional Approach ◽

Vertical Slice ◽

Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model

PeerJ ◽

10.7717/peerj.5643 ◽

2018 ◽

Vol 6 ◽

pp. e5643 ◽

Cited By ~ 2

Author(s):

Fiona Chong ◽

Matthew Spencer

Keyword(s):

Data Analysis ◽

Regression Model ◽

Compositional Data ◽

Environmental Gradients ◽

Multinomial Regression ◽

Point Count ◽

Compositional Approach ◽

Multinomial Regression Model ◽

Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.

O5A.6 Objectively assessed arm elevation and the course of neck and shoulder pain during a 2-year follow-up: a compositional approach

Occupational and Environmental Medicine ◽

10.1136/oem-2019-epi.115 ◽

2019 ◽

Vol 76 (Suppl 1) ◽

pp. A42.3-A43

Author(s):

Suzanne Merkus ◽

Lars-Kristian Lunde ◽

Markus Koch ◽

Stein Knardahl ◽

Kaj Bo Veiersted

Keyword(s):

Data Analysis ◽

Shoulder Pain ◽

Compositional Data ◽

Healthcare Personnel ◽

Compositional Approach ◽

Neck And Shoulder Pain ◽

Statistical Analysis Method ◽

Arm Elevation

PurposeTo use a compositional data analysis approach and objective exposure assessments to study the association between the duration of arm elevation and the course of neck and shoulder pain (NSP) during a 2-year follow-up in physically demanding occupations.MethodsConstruction (n=59) and healthcare (n=59) employees wore accelerometers on the dominant upper-arm during a full working day at baseline. Objective assessments using accelerometers addresses biases found in previous studies that estimate duration of arm elevation with self-reports. At baseline and every 6 months for two years, participants reported on NSP (scale 0–3). Duration of arm elevation within predefined ranges (<30°; 30–60°; ≥60) formed the parts of the composition. Compositional data analysis is a new statistical analysis method within occupational health and it is the correct way of analysing data with a compositional nature. The associations between the relative importance of the duration within the levels of arm elevation and the course of NSP during the 2-year follow-up were estimated with compositional linear mixed models, adjusted for confounders.ResultsIn non-adjusted analyses, only duration arm elevation <30° was associated with NSP at baseline (β = 0.37; p=0.015). Duration arm elevation <30° had a tendency to be associated with an improvement in NSP over the 2-year follow-up (<30°*time (β=-0.07; p=0.089)). Neither duration 30–60° nor ≥60 were associated with the course of NSP during follow-up. After adjusting for confounders, none of the durations of arm elevation were associated with the course of NSP over the 2-year period (<30° and NSP (β = 0.20; p=0.126); <30°*time (β=-0.06; p=0.097)).ConclusionAmong construction and healthcare personnel, duration of working in awkward arm elevation postures was not associated with the course of NSP over a 2-year period. Arm elevation alone, without considering force exertion, may not be sufficient to influence the course of NSP.

Changes in Sedentary Behavior Patterns During the Transition from Childhood to Adolescence and Their Association with Adiposity: A Prospective Study Based on Compositional Data Analysis

10.21203/rs.3.rs-567206/v2 ◽

2021 ◽

Author(s):

Lukáš Rubín ◽

Aleš Gába ◽

Jana Pelclová ◽

Nikola Štefelová ◽

Lukáš Jakubec ◽

...

Keyword(s):

Data Analysis ◽

Sedentary Behavior ◽

Fat Mass ◽

Compositional Data ◽

Longitudinal Design ◽

Pediatric Population ◽

Compositional Approach ◽

Sedentary Bouts

Abstract Background: To date, no longitudinal study using a compositional approach has examined sedentary behavior (SB) patterns in relation to adiposity in the pediatric population. Therefore, our aims were to (1) investigate the changes in SB patterns and adiposity from childhood to adolescence, (2) analyze the prospective compositional associations between changes in SB patterns and adiposity, and (3) estimate the changes in adiposity associated with substituting SB with physical activity (PA) of different intensities.Methods: The study presents a longitudinal design with a 5-year follow-up. A total of 88 participants (61% girls) were included in the analysis. PA and SB were monitored for seven consecutive days using a hip-worn accelerometer. Adiposity markers (fat mass percentage [FM%], fat mass index [FMI], and visceral adiposity tissue [VAT]) were assessed using the multi-frequency bioimpedance analysis. The prospective associations were examined using compositional data analysis. Results: Over the follow-up period, the proportion of time spent in total SB increased by 154.8 min/day (p < 0.001). The increase in total SB was caused mainly by an increase in middle and long sedentary bouts, as these SB periods increased by 79.8 min/day and 62 min/day (p < 0.001 for both), respectively. FM%, FMI, and VAT increased by 2.4 percent points, 1.0 kg/m2, and 31.5 cm2 (p < 0.001 for all), respectively. Relative to the remaining movement behaviors, the increase in time spent in middle sedentary bouts was significantly associated with higher FM% (βilr1 = 0.27, 95% confidence interval [CI]: 0.02 to 0.53) at follow-up. Lower VAT by 3.3% (95% CI: 0.8 to 5.7), 3.8% (95% CI: 0.03 to 7.4), 3.9% (95% CI: 0.8 to 6.9), and 3.8% (95% CI: 0.7 to 6.9) was associated with substituting 15 min/week spent in total SB and in short, middle, and long sedentary bouts, respectively, with an equivalent amount of time spent in vigorous PA.Conclusions: This study showed unfavorable changes in SB patterns and adiposity status in the transition from childhood to adolescence. Incorporating high-intensity PA at the expense of SB appears to be an appropriate approach to reduce the risk of excess adiposity in the pediatric population.

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

10.1101/104935 ◽

2017 ◽

Cited By ~ 4

Author(s):

Thomas Quinn ◽

Mark F. Richardson ◽

David Lovell ◽

Tamsyn Crowley

Keyword(s):

Data Analysis ◽

Relative Abundance ◽

Compositional Data ◽

Life Sciences ◽

Genomic Data ◽

R Package ◽

Computationally Efficient ◽

Abundance Data ◽

AbstractIn the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.

Changes in sedentary behavior patterns during the transition from childhood to adolescence and their association with adiposity: a prospective study based on compositional data analysis

Archives of Public Health ◽

10.1186/s13690-021-00755-5 ◽

2022 ◽

Vol 80 (1) ◽

Author(s):

Lukáš Rubín ◽

Aleš Gába ◽

Jana Pelclová ◽

Nikola Štefelová ◽

Lukáš Jakubec ◽

...

Keyword(s):

Data Analysis ◽

Sedentary Behavior ◽

Fat Mass ◽

Compositional Data ◽

Longitudinal Design ◽

Pediatric Population ◽

Compositional Approach ◽

Sedentary Bouts

Abstract Background To date, no longitudinal study using a compositional approach has examined sedentary behavior (SB) patterns in relation to adiposity in the pediatric population. Therefore, our aims were to (1) investigate the changes in SB patterns and adiposity from childhood to adolescence, (2) analyze the prospective compositional associations between changes in SB patterns and adiposity, and (3) estimate the changes in adiposity associated with substituting SB with physical activity (PA) of different intensities. Methods The study presents a longitudinal design with a 5-year follow-up. A total of 88 participants (61% girls) were included in the analysis. PA and SB were monitored for seven consecutive days using a hip-worn accelerometer. Adiposity markers (fat mass percentage [FM%], fat mass index [FMI], and visceral adiposity tissue [VAT]) were assessed using the multi-frequency bioimpedance analysis. The prospective associations were examined using compositional data analysis. Results Over the follow-up period, the proportion of time spent in total SB increased by 154.8 min/day (p < 0.001). The increase in total SB was caused mainly by an increase in middle and long sedentary bouts, as these SB periods increased by 79.8 min/day and 62.0 min/day (p < 0.001 for both), respectively. FM%, FMI, and VAT increased by 2.4% points, 1.0 kg/m2, and 31.5 cm2 (p < 0.001 for all), respectively. Relative to the remaining movement behaviors, the increase in time spent in middle sedentary bouts was significantly associated with higher FM% (βilr1 = 0.27, 95% confidence interval [CI]: 0.02 to 0.53) at follow-up. Lower VAT by 3.3% (95% CI: 0.8 to 5.7), 3.8% (95% CI: 0.03 to 7.4), 3.9% (95% CI: 0.8 to 6.9), and 3.8% (95% CI: 0.7 to 6.9) was associated with substituting 15 min/week spent in total SB and in short, middle, and long sedentary bouts, respectively, with an equivalent amount of time spent in vigorous PA. Conclusions This study showed unfavorable changes in SB patterns and adiposity status in the transition from childhood to adolescence. Incorporating high-intensity PA at the expense of SB appears to be an appropriate approach to reduce the risk of excess adiposity in the pediatric population.

Compositional uncertainty should not be ignored in high-throughput sequencing data analysis

Austrian Journal of Statistics ◽

10.17713/ajs.v45i4.122 ◽

2016 ◽

Vol 45 (4) ◽

pp. 73-87 ◽

Cited By ~ 32

Author(s):

Gregory Brian Gloor ◽

Jean M. Macklaim ◽

Michael Vu ◽

Andrew D. Fernandes

Keyword(s):

Data Analysis ◽

High Throughput ◽

False Positive ◽

High Throughput Sequencing ◽

In Vitro Selection ◽

Compositional Data ◽

Dirichlet Distribution ◽

Compositional Approach ◽

Log Ratio

High throughput sequencing generates sparse compositional data, yet these datasets are rarely analyzed using a compositional approach. In addition, the variation inherent in these datasets is rarely acknowledged, but ignoring it can result in many false positive inferences. We demonstrate that examination of point estimates of the data can result in false positive results, even with appropriate zero replacement approaches, using an in vitro selection dataset with an outside standard of truth. The variation inherent in real high-throughput sequencing datasets is demonstrated, and we show that this varia- tion can be approximated, and hence accounted for, by Monte-Carlo sampling from the Dirichlet distribution. This approximation when used by itself is itself problematic, but becomes useful when coupled with a log-ratio approach commonly used in compositional data analysis. Thus, the approach illustrated here that merges Bayesian estimation with principles of compositional data analysis should be generally useful for high-dimensional count compositional data of the type generated by high throughput sequencing.

A study on prospective associations between adiposity and 7-year changes in movement behaviors among older women based on compositional data analysis

BMC Geriatrics ◽

10.1186/s12877-021-02148-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jana Pelclová ◽

Nikola Štefelová ◽

Timothy Olds ◽

Dorothea Dumuid ◽

Karel Hron ◽

...

Keyword(s):

Older Women ◽

Compositional Data ◽

Elderly Women ◽

Bioelectrical Impedance ◽

Impedance Analysis ◽

Movement Behavior ◽

Least Squares Regression ◽

Longitudinal Changes ◽

Compositional Approach

Abstract Introduction It is unclear whether adiposity leads to changes in movement behaviors, and there is a lack of compositional analyses of longitudinal data which focus on these associations. Using a compositional approach, this study aimed to examine the associations between baseline adiposity and 7-year changes in physical activity (PA) and sedentary behavior (SB) among elderly women. We also explored the longitudinal associations between change in adiposity and change in movement-behavior composition. Methods This longitudinal study included 176 older women (mean baseline age 62.8 (4.1) years) from Central Europe. Movement behavior was assessed by accelerometers and adiposity was measured by bioelectrical impedance analysis at baseline and follow-up. A set of multivariate least-squares regression analyses was used to examine the associations of baseline adiposity and longitudinal changes in adiposity as explanatory variables with longitudinal changes in a 3-part movement-behavior composition consisting of SB, light PA (LPA) and moderate-to-vigorous PA (MVPA) as outcome variables. Results No significant associations were found between baseline adiposity and longitudinal changes in the movement-behavior composition (p > 0.05). We found significant associations of changes in body mass index (BMI) and fat mass percentage (FM%) with changes in the movement-behavior composition. An increase in BMI was associated with an increase of SB at the expense of LPA and MVPA (β = 0.042, p = 0.009) and with a decrease of MVPA in favor of SB and LPA (β = − 0.059, p = 0.037). An increase in FM% was significantly associated only with an increase of SB at the expense of LPA and MVPA (β = 0.019, p = 0.031). Conclusions This study did not support the assumption that baseline adiposity is associated with longitudinal changes in movement behaviors among elderly women, but we found evidence for change-to-change associations, suggesting that a 7-year increase in adiposity is associated with a concurrent increase of SB at the expense of LPA and MVPA and with a concurrent decrease of MVPA in favor of LPA and SB. Public health interventions are needed to simultaneously prevent weight gain and promote physically active lifestyle among elderly women.

Principal component analysis of financial statements. A compositional approach

Revista de Métodos Cuantitativos para la Economía y la Empresa ◽

10.46661/revmetodoscuanteconempresa.3580 ◽

2020 ◽

Vol 29 ◽

pp. 18-37

Author(s):

Miquel Carreras Simó ◽

Germà Coenders

Keyword(s):

Principal Component Analysis ◽

Compositional Data ◽

Principal Component ◽

Financial Statements ◽

Component Analysis ◽

Financial Ratios ◽

Retail Sector ◽

Financial Ratio ◽

Compositional Approach

Financial ratios are often used in principal component analysis and related techniques for the purposes of data reduction and visualization. Besides the dependence of results on ratio choice, ratios themselves pose a number of problems when subjected to a principal component analysis, such as skewed distributions. In this work, we put forward an alternative method drawn from compositional data analysis (CoDa), a standard statistical toolbox for use when data convey information about relative magnitudes, as financial ratios do. The method, referred to as the CoDa biplot, does not rely on any particular choice of financial ratio but allows researchers to visually order firms along the pairwise financial ratios for any two accounts. Non-financial magnitudes and time evolution can be added to the visualization as desired. We show an example of its application to the top chains in the Spanish grocery retail sector and show how the technique can be used to depict strategic management differences in financial structure or performance, and their evolution over time.

Changes in Sedentary Behavior Patterns During the Transition From Childhood to Adolescence and Their Association With Adiposity: a Prospective Study Based on Compositional Data Analysis

10.21203/rs.3.rs-567206/v1 ◽

2021 ◽

Author(s):

Lukáš Rubín ◽

Aleš Gába ◽

Jana Pelclová ◽

Nikola Štefelová ◽

Lukáš Jakubec ◽

...

Keyword(s):

Data Analysis ◽

Sedentary Behavior ◽

Fat Mass ◽

Compositional Data ◽

Longitudinal Design ◽

Pediatric Population ◽

Compositional Approach ◽

Sedentary Bouts

Abstract Background: To date, no longitudinal study using a compositional approach has examined sedentary behavior (SB) patterns in relation to adiposity in the pediatric population. Therefore, our aims were to (1) investigate the changes in SB patterns and adiposity from childhood to adolescence, (2) analyze the prospective compositional associations between changes in SB patterns and adiposity, and (3) estimate the changes in adiposity associated with substituting SB with physical activity (PA) of different intensities.Methods: The study presents a longitudinal design with a 5-year follow-up. A total of 88 participants (61% girls) were included in the analysis. PA and SB were monitored for seven consecutive days using a hip-worn accelerometer. Adiposity markers (fat mass percentage [FM%], fat mass index [FMI], and visceral adiposity tissue [VAT]) were assessed using the multi-frequency bioimpedance analysis. The prospective associations were examined using compositional data analysis.Results: Over the follow-up period, the proportion of time spent in total SB increased by 154.8 min/day (p < 0.001). The increase in total SB was caused mainly by an increase in middle and long sedentary bouts, as these SB periods increased by 79.8 min/day and 62 min/day (p < 0.001 for both), respectively. FM%, FMI, and VAT increased by 2.4 percent points, 1.0 kg/m2, and 31.5 cm2 (p < 0.001 for all), respectively. Relative to the remaining movement behaviors, the increase in time spent in middle sedentary bouts was significantly associated with higher FM% (βilr1 = 0.27, 95% confidence interval [CI]: 0.02 to 0.53) at follow-up. Lower VAT by 3.3% (95% CI: 0.8 to 5.7), 3.8% (95% CI: 0.03 to 7.4), 3.9% (95% CI: 0.8 to 6.9), and 3.8% (95% CI: 0.7 to 6.9) was associated with substituting 15 min/week spent in total SB and in short, middle, and long sedentary bouts, respectively, with an equivalent amount of time spent in vigorous PA.Conclusions: This study showed unfavorable changes in SB patterns and adiposity status in the transition from childhood to adolescence. Incorporating high-intensity PA at the expense of SB appears to be an appropriate approach to reduce the risk of excess adiposity in the pediatric population.